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Oceanic microorganisms explode theories of protein potential

Genes are the design component of the future -- and The Venter Institute is researching these marine treasures

Nature has so many secrets to share with us. Science is our eye and ear to the eons of diversity that surround us. What science finds is enlightening...what we do with it depends on our common sense and stewardship. A new field of research and design of energy, light and organic manufacturing is facing that challenge. And with California's exposure to, and dependence on the ocean, this micro-level marine research becomes both a community and commercial trend worth watching.

The Wonder of a Green (and Blue) :-)

"We've been missing as much as 99 percent of the life forms and biology out there," says genomics pioneer Craig Venter who is circling the globe in his yacht to collect ocean samples for genomic analysis along the way.

The unexpected level of diversity suggests that despite the nearly 200 organisms that have been sequenced to date, researchers have just begun to scratch the surface of the earth's genetic repertoire.

Microorganisms make up the bulk of life on Earth, playing a major role in carbon cycling and other global energy cycles. Yet because only about 1 percent of the organisms can be grown in a lab, identifying and understanding these microscopic creatures is difficult. Now, ever-improving gene-sequencing methods developed over the past few years offer microbiologists a new tool with which to study the other 99 percent. Scientists can extract the genetic material from a drop of seawater and then sequence that DNA, deriving genomic clues into all the organisms living in that environment.

In 2003, Venter embarked on an expedition that followed the route of the British ship the Challenger, a research voyage that catalogued 5,000 new marine species in the late 1800s. The crew traveled nearly 6,000 miles aboard Venter's yacht, collecting samples of surface water every 200 miles.

The first set of results, published this week in three papers in the journal PLoS Biology, revealed six million new proteins, doubling the number of known protein sequences. "Everywhere we sampled, we found new proteins," says Venter.

This new collection of proteins should shed light on how proteins evolved, and perhaps even hint at the genetics of our earliest ancestral organisms. "With a diverse collection of proteins, you can build a phylogenetic tree and try to infer function and how it evolved," says Shibu Yooseph, a scientist at the J. Craig Venter Institute, in Rockville, MD, and the lead author of one of the PLoS Biology papers. "For every family we've looked at, both the number and diversity of new proteins was really unexpected."

One of the most abundant types of protein identified in the study comes from proteorhodopsins, molecules that resemble light-sensing proteins in the human eye. They appear to endow microorganisms with an alternative mechanism to photosynthesis in order to generate energy from light.

Researchers also found that slight changes in the protein affect the wavelength of light the organism can absorb: the particular variant an organism possesses seems to follow the predominant color of water in its environment. On the coast, for example, where the water is green, organisms can mostly absorb green light. But in the deep sea, where the water is blue, organisms can mostly absorb blue light.

The findings are challenging the notion of species in microorganisms. "When you look at microbes, they don't appear to be individual species," says Douglas Rusch, also a scientist at the Venter Institute and an author of one of the papers. "It seems to be a complex mixture, which we describe as subtypes, which are adapted to a particular environment."

"Microbial communities are almost like a superorganism, where each microbe is contributing to community as a whole," says Weinstock. "We really need to characterize the metagenome and analyze the genes and protein products as an aggregate."

Venter and others eventually hope to find proteins that can be co-opted to create novel bacterial machines--proteins involved in hydrogen production or carbon fixation, for example, that could one day be engineered to boost the carbon-fixing capacity of the ocean or to create fuel-producing bacteria. "Genes are the design component of the future," says Venter.

The California Connection

UC San Diego Makes Venter Institute's Global Ocean Sampling (GOS) Expedition Microbial Metagenomic Data and Computational Tools Available to Scientists Worldwide
Scientists and engineers at the University of California, San Diego and the J. Craig Venter Institute (JCVI) have flipped the virtual switch on the first cyberinfrastructure customized to serve the marine microbial metagenomics community. At the heart of the cyberinfrastructure is a new, high-performance computer and storage complex funded by the Gordon and Betty Moore Foundation and located in UC San Diego’s Atkinson Hall, headquarters of the California Institute for Telecommunications and Information Technology (Calit2), a partnership of UC San Diego and UC Irvine.

“A new cyberinfrastructure architecture is required to support the field of genomics as it transitions to the study of metagenomics,” said CAMERA principal investigator Larry Smarr, professor of computer science and engineering at UC San Diego and director of Calit2. “The infrastructure will create a virtual domain for global data and knowledge sharing by this emerging research community.”

The J. Craig Venter Institute (JCVI) is a not-for-profit research institute dedicated to the advancement of the science of genomics; the understanding of its implications for society; and the communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the Institute, through its two divisions—The Institute for Genomic Research (TIGR) and The Center for the Advancement of Genomics (TCAG) is home to more than 500 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, high-throughput DNA sequencing, information technology, functional genomics, and genomic and environmental policy research.

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